From 14b631b0009e07f36623ec878345b2a3b6c39774 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Wed, 11 Feb 2009 15:10:08 +0000
Subject: [PATCH] removed globals
---
fslstats.cc | 67 +++++++++++++++++++----------------------------------
1 file changed, 24 insertions(+), 43 deletions(-)
diff --git a/fslstats.cc b/fslstats.cc
index 58f7c77..0ee67f5 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -2,7 +2,7 @@
Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
- Copyright (C) 2003-2007 University of Oxford */
+ Copyright (C) 2003-2009 University of Oxford */
/* CCOPYRIGHT */
@@ -11,13 +11,7 @@
#include "newimage/costfns.h"
#include "utils/fsl_isfinite.h"
-
using namespace NEWIMAGE;
-using namespace MISCMATHS;
-
-bool masks_used=false;
-bool lthr_used=false;
-bool uthr_used=false;
void print_usage(const string& progname) {
cout << "Usage: fslstats <input> [options]" << endl << endl;
@@ -49,7 +43,6 @@ void print_usage(const string& progname) {
cout << "Note - thresholds are not inclusive ie lthresh<allowed<uthresh" << endl;
}
-
// Some specialised nonzero functions just for speedup
// (it avoids generating masks when not absolutely necessary)
@@ -119,29 +112,18 @@ double nonzerostddev(const volume4D<float>& vol)
return std::sqrt(var);
}
-int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin,float& lthr, float& uthr)
+int generateNonZeroMask(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &input)
{
- if (!lthr_used) { lthr=vin.min()-1; }
- if (!uthr_used) { uthr=vin.max()+1; }
- mask = binarise(vin,lthr,uthr,exclusive);
- if (mask.tsize()!=1) {
- masknz.reinitialize(mask.xsize(),mask.ysize(),mask.zsize(),mask.tsize());
- for (int t=mask.mint(); t<=mask.maxt(); t++)
- masknz[t]=((binarise(vin[t],0.0f, 0.0f)-1.0f)*-1.0f*mask[t]);
- }
- else masknz = (binarise(vin,0.0f, 0.0f)-1.0f)*-1.0f*mask[0];
+ masknz.reinitialize(mask.xsize(),mask.ysize(),mask.zsize(),input.tsize());
+ for (int t=input.mint(); t<=input.maxt(); t++)
+ masknz[t]=((binarise(input[t],0.0f, 0.0f)-1.0f)*-1.0f*mask[t % mask.tsize()]);
return 0;
}
-int generate_masks(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin)
+int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &input,float& lthr, float& uthr)
{
- if (mask.tsize()!=1) {
- masknz.reinitialize(mask.xsize(),mask.ysize(),mask.zsize(),mask.tsize());
- for (int t=mask.mint(); t<=mask.maxt(); t++)
- masknz[t]=((binarise(vin[t],0.0f, 0.0f)-1.0f)*-1.0f*mask[t]);
- }
- else masknz = (binarise(vin,0.0f, 0.0f)-1.0f)*-1.0f*mask[0];
- return 0;
+ mask = binarise(input,lthr,uthr,exclusive);
+ return generateNonZeroMask(mask,masknz,input);
}
int fmrib_main_float(int argc, char* argv[])
@@ -155,7 +137,8 @@ int fmrib_main_float(int argc, char* argv[])
volume4D<float> vol, mask, masknz;
read_volume4D(vol,argv[1]);
- float lthr=0, uthr=0; // these initial values are not used
+ float lthr(vol.min()-1);
+ float uthr=(vol.max()+1);
int narg=2;
string sarg;
@@ -170,10 +153,10 @@ int fmrib_main_float(int argc, char* argv[])
if (!isfinite((double)vol(x,y,z,t)))
vol(x,y,z,t)=0;
} else if (sarg=="-m") {
- if (masks_used) cout << vol.mean(mask) << " ";
+ if (mask.nvoxels()>0) cout << vol.mean(mask) << " ";
else cout << vol.mean() << " ";
} else if (sarg=="-M") {
- if (masks_used) cout << vol.mean(masknz) << " ";
+ if (masknz.nvoxels()>0) cout << vol.mean(masknz) << " ";
else {
double nzmean=0;
nzmean = nonzeromean(vol);
@@ -182,7 +165,7 @@ int fmrib_main_float(int argc, char* argv[])
} else if (sarg=="-X") {
ColumnVector coord(4);
coord(4)=1.0;
- if (masks_used) {
+ if (mask.nvoxels()>0) {
coord(1) = vol.mincoordx(mask);
coord(2) = vol.mincoordy(mask);
coord(3) = vol.mincoordz(mask);
@@ -197,7 +180,7 @@ int fmrib_main_float(int argc, char* argv[])
} else if (sarg=="-x") {
ColumnVector coord(4);
coord(4)=1.0;
- if (masks_used) {
+ if (mask.nvoxels()>0) {
coord(1) = vol.maxcoordx(mask);
coord(2) = vol.maxcoordy(mask);
coord(3) = vol.maxcoordz(mask);
@@ -305,7 +288,7 @@ int fmrib_main_float(int argc, char* argv[])
}
mask.binarise(0.5);
- generate_masks(mask,masknz,vol);
+ generateNonZeroMask(mask,masknz,vol);
if (mask.tsize()!=1) vol*=mask;
else vol*=mask[0];
} else if (sarg=="-l") {
@@ -316,7 +299,6 @@ int fmrib_main_float(int argc, char* argv[])
cerr << "Must specify an argument to -l" << endl;
exit(2);
}
- lthr_used=true;
generate_masks(mask,masknz,vol,lthr,uthr);
vol*=mask;
} else if (sarg=="-u") {
@@ -327,13 +309,12 @@ int fmrib_main_float(int argc, char* argv[])
cerr << "Must specify an argument to -u" << endl;
exit(2);
}
- uthr_used=true;
generate_masks(mask,masknz,vol,lthr,uthr);
vol*=mask;
} else if (sarg=="-a") {
vol = abs(vol);
} else if (sarg=="-v") {
- if (masks_used) {
+ if (mask.nvoxels()>0) {
cout << (long int) mask.sum() << " "
<< mask.sum() * vol.xdim() * vol.ydim() * vol.zdim() << " ";
} else {
@@ -341,7 +322,7 @@ int fmrib_main_float(int argc, char* argv[])
<< vol.nvoxels() * vol.tsize() * vol.xdim() * vol.ydim() * vol.zdim() << " ";
}
} else if (sarg=="-V") {
- if (masks_used) {
+ if (masknz.nvoxels()>0) {
cout << (long int) masknz.sum() << " "
<< masknz.sum() * vol.xdim() * vol.ydim() * vol.zdim() << " ";
} else {
@@ -354,19 +335,19 @@ int fmrib_main_float(int argc, char* argv[])
// hidden debug option!
cout << vol.sum() << " ";
} else if (sarg=="-s") {
- if (masks_used) cout << vol.stddev(mask) << " ";
+ if (mask.nvoxels()>0) cout << vol.stddev(mask) << " ";
else cout << vol.stddev() << " ";
} else if (sarg=="-S") {
- if (masks_used) {
+ if (masknz.nvoxels()>0) {
cout << vol.stddev(masknz) << " ";
} else {
cout << nonzerostddev(vol) << " ";
}
} else if (sarg=="-r") {
- if (masks_used) cout << vol.robustmin(mask) << " " << vol.robustmax(mask) << " ";
+ if (mask.nvoxels()>0) cout << vol.robustmin(mask) << " " << vol.robustmax(mask) << " ";
else cout << vol.robustmin() << " " << vol.robustmax() << " ";
} else if (sarg=="-R") {
- if (masks_used) cout << vol.min(mask) << " " << vol.max(mask) << " ";
+ if (mask.nvoxels()>0) cout << vol.min(mask) << " " << vol.max(mask) << " ";
else cout << vol.min() << " " << vol.max() << " ";
} else if (sarg=="-c") {
ColumnVector cog(4);
@@ -395,7 +376,7 @@ int fmrib_main_float(int argc, char* argv[])
cerr << "Percentile must be between 0 and 100" << endl;
exit(1);
}
- if (masks_used) cout << vol.percentile((float) n/100.0, mask) << " ";
+ if (mask.nvoxels()>0) cout << vol.percentile((float) n/100.0, mask) << " ";
else cout << vol.percentile((float) n/100.0) << " ";
} else if (sarg=="-P") {
float n;
@@ -429,7 +410,7 @@ int fmrib_main_float(int argc, char* argv[])
cerr << "Must specify at least 1 bin" << endl;
exit(1);
}
- if (masks_used) {
+ if (mask.nvoxels()>0) {
cout << vol.histogram(nbins,vol.min(),vol.max(),mask) << " ";
} else {
cout << vol.histogram(nbins,vol.min(),vol.max()) << " ";
@@ -464,7 +445,7 @@ int fmrib_main_float(int argc, char* argv[])
cerr << "Must specify the histogram maximum intensity" << endl;
exit(2);
}
- if (masks_used) {
+ if (mask.nvoxels()>0) {
cout << vol.histogram(nbins,min,max,mask) << " ";
} else {
cout << vol.histogram(nbins,min,max) << " ";
--
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